1.3 THE NEW BIOLOGY AND THE MOUSE MODEL

1.3.1 All mammals have closely related genomes

The movement of mouse genetics from a backwater field of study to the
forefront of modern biomedical research was catalyzed by the recombinant DNA
revolution, which began 20 years ago and has been accelerating in pace ever since.
With the ability to isolate cloned copies of genes and to compare DNA sequences
from different organisms came the realization that mice and humans (as well as all
other placental mammals) are even more similar genetically than they were
thought to be previously. An astounding finding has been that all human genes
have counterparts in the mouse genome which can almost always be recognized by
cross-species hybridization. Thus, the cloning of a human gene leads directly to the
cloning of a mouse homolog which can be used for genetic, molecular, and
biochemical studies that can then be extrapolated back to an understanding of the
function of the human gene. In only a subset of cases are mammalian genes
conserved within the genomes of Drosophila or C. elegans.

This result should not be surprising in light of current estimates for the time of
divergence of mice, flies and nematodes from the evolutionary line leading to
humans. In general, three types of information have been used to build
phylogenetic trees for distantly related members of the animal kingdom 
paleontological data based on radiodated fossil remains, sequence comparisons of
highly conserved proteins, and direct comparisons of the most highly conserved
genomic sequences, namely the ribosomal genes. Unfortunately, flies (Drosophila)
and nematodes (C. elegans) diverged apart from the line leading to mammals just prior
to the time of the earliest fossil records in the Cambrian period which occurred 570
million years ago. The divergence of
mice and people occurred relatively recently at 60 million years before present (see
Section 2.2.1). These numbers are presented graphically in
Figure 1.3,
where a quick glance serves to drive home the fact that humans and mice are ten times more
closely related to each other than either is to flies or nematodes.

Although the haploid chromosome number associated with different
mammalian species varies tremendously, the haploid content of mammalian DNA
remains constant at approximately three billion basepairs. It is not only the size of
the genome that has remained constant among mammals; the underlying genomic
organization (discussed in
Chapter 5) has also remained the same as well. Large
genomic segments  on average, 10-20 million basepairs  have been
conserved virtually intact between mice, humans, and other mammals as well. In fact, the
available data suggest that a rough replica of the human genome could be built by
simply breaking the mouse genome into 130-170 pieces and pasting them back
together again in a new order
(Nadeau, 1984;
Copeland et al., 1993). Although all
mammals are remarkably similar in their overall body plan, there are some
differences in the details of both development and metabolism, and occasionally
these differences can prevent the extrapolation of mouse data to humans and vice
versa
(Erickson, 1989). Nevertheless, the mouse has proven itself over and over
again as being the model experimental animal par excellence for studies of nearly all
aspects of human genetics.

1.3.2 The mouse is an ideal model organism

Among mammals, the mouse is ideally suited for genetic analysis. First, it is
among the smallest mammals known with adult weights in the range of 25-40
g, 2,000-3,000-fold lighter than the average human adult. Second, it has a short
generation time  on the order of 10 weeks from being born to giving birth. Third,
females breed prolifically in the lab with an average of 5-10 pups per litter and an
immediate postpartum estrus. Fourth, an often forgotten advantage is the fact that
fathers do not harm their young, and thus breeding pairs can be maintained
together after litters are born. Fifth, for developmental studies, the deposition of a
vaginal plug allows an investigator to time all pregnancies without actually
witnessing the act of copulation and, once again, without removing males from the
breeding cage. Finally, most laboratory-bred strains are relatively docile and easy to
handle.

The high resolution genetic studies to be discussed later in this book require the
analysis of large numbers of offspring from each of the crosses under analysis. Thus,
a critical quotient in choosing an organism can be expressed as the number of
animals bred per square meter of animal facility space per year. For mice, this
number can be as high as 3,000 pups/m2 including the actual space for racks (five
shelves high) as well as the inter-rack space as well. All of the reasons listed here
make the mouse an excellent species for genetic analysis and have helped to make it
the major model for the study of human disease and normative biology.

1.3.3 Manipulation of the mouse genome and micro-analysis

The close correspondence discovered between the genomes of mice and humans
would not, in and of itself, have been sufficient to drive workers into mouse
genetics without the simultaneous development, during the last decade, of
increasingly more sophisticated tools to study and manipulate the embryonic
genome. Today, genetic material from any source (natural, synthetic or a
combination of the two) can be injected directly into the nuclei of fertilized eggs; two
or more cleavage-stage embryos can be teased apart into component cells and put
back together again in new "chimeric" combinations; nuclei can be switched back
and forth among different embryonic cytoplasma; embryonic cells can be placed into
tissue culture, where targeted manipulation of individual genes can be
accomplished before these cells are returned to the embryo proper. Genetically
altered live animals can be obtained subsequent to all of these procedures, and these
animals can transmit their altered genetic material to their offspring. The protocols
involved in all of these manipulations of embryos and genomes have become well-established and cookbook manuals
(Joyner, 1993;
Wassarman and DePamphilis, 1993;
Hogan et al., 1994) as well as a video guide to the protocols involved
(Pedersen et al., 1993) have been published.

While it is likely that none of these manipulations has yet been applied to
human embryos and genomes, it is ethical, rather than technical, roadblocks that
impede progress in this direction. The mental image invoked is of a far more
sophisticated technology than the so-called futuristic scenario of embryo farms
described in Huxley's Brave New World
(1932).

Progress has also been made at the level of molecular analysis within the
developing embryo. With the polymerase chain reaction (PCR) protocol, DNA and
RNA sequences from single cells can be characterized, and enhanced versions of the
somewhat older techniques of in situ hybridization and immuno-staining allow
investigators to follow the patterns of individual gene expression through the four
dimensions of space and time
(Wassarman and DePamphilis, 1993;
Hogan et al.,
1994). In addition, with the omnipresent micro-techniques developed across the
field of biochemistry, the traditional requirement for large research animals like the
rat, rabbit, or guinea pig has all but evaporated.

1.3.4 High resolution genetics

Finally, with the automation and simplification of molecular assays that has
occurred over the last several years, it has become possible to determine
chromosomal map positions to a very high degree of resolution. Genetic studies of
this type are relying increasingly on extremely polymorphic microsatellite loci
(Section 8.3) to produce anchored linkage maps
(Chapter 9), and large insert cloning
vectors  such as yeast artificial chromosomes (YACs)  to move from the
observation of a phenotype, to a map of the loci that cause the phenotype, to clones of the loci themselves
(Section 10.3).
Thus, many of the advantages that were once uniquely available to investigators
studying lower organisms, such as flies and worms, can now be applied to the
mouse through the three-way marriage of genetics, molecular biology, and
embryology represented in
Figure 1.4 .
It is the intention of this book to provide the
conceptual framework and practical basis for the new mouse genetics.